Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,734,543	(C)8→9	coding (492/732 nt)	pgeF ←	polyphenol oxidase YfiH

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,734,535	1	.	C	96.4%	92.9 / ‑3.1	28	coding (500/732 nt)	pgeF	polyphenol oxidase YfiH
Reads supporting (aligned to +/- strand):  ref base . (0/1);  new base C (18/9);  total (18/10)
Fisher's exact test for biased strand distribution p-value = 3.57e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.76e-01

GCCGCCGAAAATTTGCTCAACACCCACGTTCGCCAGACGCTGCCGGGCAAGCTGATAAATATCCGCCAGATACTTATCACCATGCTGAATGAAAGCTGCACTTGCTTTAGCGTCTACTGCCATAAACGCCTCGCGAA‑CCT‑CCCCCCCCACTTCGAACGCGCGTGGACCAATTGCCGGCCCTAACCAGGCGAGAATATTTTCCGGATTATCAGCAAAACAGGAAACCGTCTCTTCCAGCACGCCTGCGCACAGTCCACGCCAGCCAGCA  >  NC_000913/2734396‑2734663                                                                                                                                              |                                                                                                                                 gccgccGAAAATTTGCTCAACACCCACGTTCGCCAGACGCTGCCGGGCAAGCTGATAAATATCCGCCAGATACTTATCACCATGCTGAATGAAAGCTGCACTTGCTTTGGCGTCTACTGCCATAAACGCCTCGCGAA‑CCt                                                                                                                                   >  2:349408/1‑140 (MQ=255)                                                   gCTGATAAATATCCGCCAGATACTTATCACCATGCTGAATGAAAGCTGCACTTGCTTTAGCGTCTACTGCCATAAACGCCTCGCGAA‑CCTCCCCCCCCCACTTCGAACGCGCGTGGACCAATTGCCGGCCCTAACCAGGc                                                                                 <  1:349408/140‑1 (MQ=255)                                                                cGCCAGATACTTATCACCATGCTGAATGAAAGCTGCACTTGCTTTAGCGTCTACTGCCATAAACGCCTCGCGAA‑CCTCCCCCCCCCACTTCGAACGCGCGTGGACCAATTGCCGGCCCTAACCAGGCGAGAATATTTTcc                                                                    <  1:58241/140‑1 (MQ=255)                                                                      aTACTTATCACCATGCTGAATGAAAGCTGCACTTGCTTTAGCGTCTACTGCCATAAACGCCTCGCGAA‑CCTCCCCCCCCCACTTCGAACGCCCGTGGACCAATTACCGCCCCTAACCAGGCGCGAATATTTACCGGATTa                                                              >  2:361160/1‑140 (MQ=255)                                                                            agcccaaTGCTGAATGAAAGCTGCACTTGCTTTAGCGTCTACTGCCATAAACGCCTCGCGAA‑CCTCCCCCCCCCACTTCGAACGCGCGTGGACCAATTGCCGGCCCTAACCAGGCGAGAATATTTTCCGGATTATCAGCa                                                        <  2:66806/134‑1 (MQ=255)                                                                             tCACCATGCTGAATGAAAGCTGCACTTGCTTTAGCGTCTACTGCCATAAACGCCTCGCGAA‑CCTCCCCCCCCCACTTCGAACGCGCGTGGACCAGTTGCCGGCCCTAACCAGGCGAGAATATTTTCCGGATTATCAGCaa                                                       >  2:785722/1‑140 (MQ=255)                                                                               aCCATGCTGAATGAAAGCTGCACTTGCTTTAGCGTCTACTGCCATAAACGCCTCGCGAA‑CCTCCCCCCCCCACTTCGAACGCGCGTGGACCAATTGCCGGCCCTAACCAGGCGAGAATATTTTCCGGATTATCAGCaaaa                                                     >  1:74816/1‑140 (MQ=255)                                                                               aCCATGCTGAATGAAAGCTGCACTTGCTTTAGCGTCTACTGCCATAAACGCCTCGCGAA‑CCTCCCCCCCCCACTTCGAACGCGCGTGGACCAATTGCCGGCCCTAACCAGGCGAGAATATTTTCCGGATTATCAGCaaaa                                                     >  2:432586/1‑140 (MQ=255)                                                                                ccATGCTGAATGAAAGCTGCACTTGCTTTAGCGTCTACTGCCATAAACGCCTCGCGAA‑CCTCCCCCCCCCACTTCGAACGCGCGTGGACCAATTGCCGGCCCTAACCAGGCGAGAATATTTTCCGGATTATCAGCAAAAc                                                    >  1:712672/1‑140 (MQ=255)                                                                                 cATGCTGAATGAAAGCTGCACTTGCTTTAGCGTCTACTGCCATAAACGCCTCGCGAA‑CCTCCCCCCCCCACTTCGAACGCGCGTGGACCAATTGCCGGCCCTAACCAGGCGAGAATATTTTCCGGATTATCAGCAAAACa                                                   <  1:432586/140‑1 (MQ=255)                                                                                   tGCTGAATGAAAGCTGCACTTGCTTTAGCGTCTACTGCCATAAACGCCTCGCGAA‑CCTCCCCCCCCCACTTCGAACGCGCGTGGACCAATTGCCGGCCCTAACCAGGCGAGAATATTTTCCGGATTATCAGCAAAACAgg                                                 >  2:496989/1‑140 (MQ=255)                                                                                    gCTGAATGAAAGCTGCACTTGCTTTAGCGTCTACTGCCATAAACGCCTCGCGAA‑CCTCCCCCCCCCACTTCGAACGCGCGTGGACCAATTGCCGGCCCTAACCAGGCGAGAATATTTTCCGGATTATCAGCAAAACAGGa                                                >  2:18807/1‑140 (MQ=255)                                                                                     cTGAATGAAAGCTGCACTTGCTTTAGCGTCTACTGCCATAAACGCCTCGCGAA‑CCTCCCCCCCCCACTTCGAACGCGCGTGGACCAATTGCCGGCCCTAACCAGGCGAGAATATTTTCCGGATTATCAGCAAAACAGGaa                                               <  1:496989/140‑1 (MQ=255)                                                                                      tgaatgaaAGCTGCACTTGCTTTAGCGTCTACTGCCATAAACGCCTCGCGAA‑CCTCCCCCCCCCACTTCGAACGCGCGTGGACCAATTGCCGGCCCTAACCAGGCGAGAATATTTTCCGGATTATCAGCAAAACAGGaaa                                              <  1:26657/140‑1 (MQ=255)                                                                                        aatgaaAGCTGCACTTGCTTTAGCGTCTACTGCCATAAACGCCTCGCGAA‑CCTCCCCCCCCCACTTCGAACGCGCGTGGACCAATTGCCGGCCCTAACCAGGCGAGAATATTTTCCGGATTATCAGCAAAACAGGAAAcc                                            >  1:715827/1‑140 (MQ=255)                                                                                          tgaaAGCTGCACTTGCTTTAGCGTCTACTGCCATAAACGCCTCGCGAA‑CCTCCCCCCCCCACTTCGAACGCGCGTGGACCAATTGCCGTCCCTAACCAGGCGAGAATATTTTCCGGATTATCAGCAAAACAGGAAACCGt                                          <  1:618903/140‑1 (MQ=255)                                                                                          tgaaAGCTGCACTTGCTTTAGCGTCTACTGCCATAAACGCCTCGCGAA‑CCTCCCCCCCCCACTTCGAACGCGCGTGGACCAATTGCCGGCCCTAACCAGGCGAGAATATTTTCCGGATTATCAGCAAAACAGGAAACCgc                                          >  2:768669/1‑139 (MQ=255)                                                                                                   cACTTGCTTTAGCGTCTACTGCCATAAACGCCTCGCGAA‑CCTCCCCCCCCCACTTCGAACGCGCGTGGACCAATTGCCGGCCCTAACCAGGCGAGAATATTTTCCGGATTATCAGCAAAACAGGAAACCGTCTCTTCCAg                                 >  1:725601/1‑140 (MQ=255)                                                                                                   cACTTGCTTTAGCGTCTACTGCCATAAACGCCTCGCGAA‑CCTCCCCCCCCCACTTCGAACGCGCGTGGACCAATTGCCGGCCCTAACCAGGCGAGAATATTTTCCGGATTATCAGCAAAACAGGAAACCGTCTCTTCCAg                                 >  1:56445/1‑140 (MQ=255)                                                                                                     cTTGCTTTAGCGTCTACTGCCATAAACGCCTCGCGAA‑CCTCCCCCCCCCACTTCGAACGCGCGTGGACCAATTGCCGGCCCTAACCAGGCGAGAATATTTTCCGGATTATCAGCAAAACAGGAAACCGTCTCTTCCAGCa                               <  2:712672/140‑1 (MQ=255)                                                                                                           ttAGCGTCTACTGCCATAAACGCCTCGCGAA‑CCTCCCCCCCCCACTTCGAACGCGCGTGGACCAATTGCCGGCCCTAACCAGGCGAGAATATTTTCCGGATTATCAGCAAAACAGGAAACCGTCTCTTCCAGCACGCCTg                         >  1:828164/1‑140 (MQ=255)                                                                                                             aGCGTCTACTGCCATAAACGCCTCGCGAA‑CCTCCCCCCCCCACTTCGAACGCGCGTGGACCAATTGCCGGCCCTAACCAGGCGAGAATATTTTCCGGATTATCAGCAAAACAGGAAACCGTCTCTTCCAg                                 >  2:722654/1‑130 (MQ=255)                                                                                                             aGCGTCTACTGCCATAAACGCCTCGCGAA‑CCTCCCCCCCCCACTTCGAACGCGCGTGGACCAATTGCCGGCCCTAACCAGGCGAGAATATTTTCCGGATTATCAGCAAAACAGGAAACCGTCTCTTCCAg                                 <  1:722654/130‑1 (MQ=255)                                                                                                               cGTCTACTGCCATAAACGCCTCGCGAACCCC‑CCCCCCCCACTTCGAACGCGCGTGGACCAATTGCCGGCCCTAACCAGGCGAGAATATTTTCCGGATTATCAGCAAAACAGGAAACCGTCTCTTCCAGCACGCCTGCGca                     <  1:768669/140‑1 (MQ=255)                                                                                                               cGTCTACTGCCATAAACGCCTCGCGAA‑CCTCCCCCCCCCACTTCGAACGCGCGTGGACCAATTGCCGGCCCTAACCAGGCGAGAATATTTTCCGGATTATCAGCAAAACAGGAAACCGTCTCTTCCAGCACGCCTGCGca                     <  1:192341/140‑1 (MQ=255)                                                                                                                   tACTGCCATAAACGCCTCGCGAA‑CCTCCCCCCCCCACTTCGAACGCGCGTGGACCAATTGCCGGCCCTAACCAGGCGAGAATATTTTCCGGATTATCAGCAAAACAGGAAACCGTCTCTTCCAGCACGCCTGCGCACAGt                 >  1:152960/1‑140 (MQ=255)                                                                                                                      tGCCATAAACGCCTCGCGAA‑CCTCCCCCCCCCACTTCGAACGCGCGTGGACCAATTGCCGGCCCTAACCAGGCGAGAATATTTTCCGGATTATCAGCAAAACAGGAAACCGTCTCTTCCAGCACGCCTGCGCACAGTCCa              >  2:432468/1‑140 (MQ=255)                                                                                                                                  cccgcgAA‑CCTCCCCCCCCCACTTCGAACCCGCGTGGACCAATTGCCGGCCCTAACCAGGCGAGAATATTTTCCGGATTATCAGCAAAACAGGAAACCGTGTCTGCCAGCACGCCTGGGCACGGTCCCCGCCAGCCAGCa  >  2:213515/3‑140 (MQ=255)                                                                                                                                  cTCGCGAA‑CCTCCCCCCCCCACTTCGAACGCGCGTGGACCAATTGCCGGCCCTAACCAGGCGAGAATATTTTCCGGATTATCAGCAAAACAGGAAACCGTCTCTTCCAGCACGCCTGCGCACAGTCCACGCCAGCCAGCa  >  2:761270/1‑140 (MQ=255)                                                                                                                                  cTCGCGAA‑CCTCCCCCCCCCACTTCGAACGCGCGTGGACCAATTGCCGGCCCTAACCAGGCGAGAATATTTTCCGGATTATCAGCAAAACAGGAAACCGTCTCTTCCAGCACGCCTGCGCACAGTCCACGCCAGCCAGCa  >  2:821348/1‑140 (MQ=255)                                                                                                                                              |                                                                                                                                 GCCGCCGAAAATTTGCTCAACACCCACGTTCGCCAGACGCTGCCGGGCAAGCTGATAAATATCCGCCAGATACTTATCACCATGCTGAATGAAAGCTGCACTTGCTTTAGCGTCTACTGCCATAAACGCCTCGCGAA‑CCT‑CCCCCCCCACTTCGAACGCGCGTGGACCAATTGCCGGCCCTAACCAGGCGAGAATATTTTCCGGATTATCAGCAAAACAGGAAACCGTCTCTTCCAGCACGCCTGCGCACAGTCCACGCCAGCCAGCA  >  NC_000913/2734396‑2734663

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑